I like rules to make some kind of sense, even if the explanation involves the way magic works and is in no way "realistic" its better than a blanket: It works like this-you think up why something that nonsensical exists.
But they do make sense. Did you have a problem with spontaneous casters in 3rd? One of their core class abilities was retraining. Swapping out spells every few levels. To cover that necessary mechanic, an in game justification was easy - just the way magic works. It's no more a mental exercise to envision power replacement in game.
Let's use the fighter for an example. Lol, our fighter, reaches 15th level, where mechanically he replaces one daily power with a 15th level daily. He replaces Brute Strike, an exploit he has used since 1st level, with Dragon's Fangs, a power which essentially is two brute strikes. He does not tangibly "lose" Brute Strike, he has simply developed a better maneuver. If you are trying to kill someone, why would you do less damage then you are now capable of doing?
But Thas, you say, Dragon's Fangs is a fairly logical replacement for Brute Strike, its basically just the power improved, THAT at least makes some sense, but what if he went for something totally different?
Well, let's see - Unyielding Avalance Death - you've gained wisdom over your career (literally, by 15th level), and you've learned that such single minded attention to delivering big damage to a single foe often leaves you vulnerable. Your experience in such melees has taught you the value of being prudent and patient, so you discard some of your old ways in favor of a more refined, but no less effective technique.
Feats? Not much problem there either. A wintertouched mage drops the feat for raging storm instead, as he has chosen more lightning and thunder powers. Does this really require a stretch to explain? The studious mage has focused on mastery of a different area of elemental power. There are, of course, a few examples you can find where it might get a bit hairy. Someone takes Linguist and decides to dump it for Power Attack. The new tactic is easy to explain, they've been training, learning, growing. But losing three known languages? Well, as a couple people have already mentioned, anyone who took a language in High School and never had much occassion to use it has long since lost that skill. Mine was German and all i can do these days is count to 10, drop a bit of foul language, or tell someone 'I shot my brother'. "Infernal? I haven't spoken that since you've known me, with all we've been through, no, I really barely remember a word. I think the runes on that door say something about saurkraut, no that can't be it..." As a DM, in that circumstance, I would give the PC a +2 to Insight to use his barely remembered smattering of Infernal to understand what the dread beast is telling the party.
In game justification requires only a very minor flexing of your creative muscle, if your group even requires it. It's not like the concept of in game justification for mechanical systems is something you've never had to do before if you play D&D (and it matters to you). Magic has always required this creative muscle reflex, we're just used to it, it's an accepted part of the game.
The mechanical need for the system is there and justifying it in game is cake, just like you do, and have always done, any number of other things - HPs, spells, knowledge of effects or conditions, etc.
